diff -Nru debian-med-1.13ubuntu1/debian/changelog debian-med-1.13.1ubuntu1/debian/changelog --- debian-med-1.13ubuntu1/debian/changelog 2012-12-05 21:32:36.000000000 +0530 +++ debian-med-1.13.1ubuntu1/debian/changelog 2012-12-13 18:22:17.000000000 +0530 @@ -1,3 +1,20 @@ +debian-med (1.13.1ubuntu1) raring; urgency=low + + * Merge from Debian unstable (LP: #1089907). Remaining changes: + - sources.list.quantal → sources.list.raring + - regenerate debian/control. + - Change libteem1-dev in Recommends to libteem-dev + for libteem1-dev -> libteem-dev transition. + + -- Vibhav Pant Thu, 13 Dec 2012 18:19:52 +0530 + +debian-med (1.13.1) unstable; urgency=low + + * Revert name change from med-pharmacy -> med-pharma + Closes: #694424 + + -- Andreas Tille Tue, 27 Nov 2012 17:37:26 +0100 + debian-med (1.13ubuntu1) raring; urgency=low * Merge from Debian unstable. Remaining changes: diff -Nru debian-med-1.13ubuntu1/debian/control debian-med-1.13.1ubuntu1/debian/control --- debian-med-1.13ubuntu1/debian/control 2012-12-05 21:28:35.000000000 +0530 +++ debian-med-1.13.1ubuntu1/debian/control 2012-12-13 18:19:23.000000000 +0530 @@ -59,7 +59,7 @@ Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, dssp, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fasttree, fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, gbrowse, gdpc, gentle, gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, neobio, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, r-cran-genabel, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, sra-toolkit, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise -Suggests: abyss, act, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, bamtools, beads, beast-mcmc, big-blast, bigsdb, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdna-db, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, concavity, conservation-code, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, edtsurf, eigensoft, elph, embassy-phylip, emboss-explorer, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fastqc, figaro, finex, fluctuate, forester, forge, galaxy, gassst, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, genometools, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, hmmer2, igv, jbrowse, jigsaw, jstreeview, kempbasu, lagan, lamarc, logol-bin, logomat-m, ltrsift, lucy, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, mosaik-aligner, mozilla-biofox, mpsqed, msatfinder, mugsy, mummergpu, murasaki, mview, ncbi-seg, ngila, norsnet, norsp, nw-align, oases, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, patristic, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phyloviz-core, phylowin, plato, prank, predictnls, predictprotein, proalign, profbval, profisis, profit, prot4est, pscan-tfbs, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatmasker, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, seqtk, sequenceconverter.app, sga, sift, smalt, snap, snpeff, soapdenovo, spice, splitstree, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tigr-glimmer-mg, tophat, trace2dbest, tracetuner, treebuilder3d, treetime, treeview, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zalign, zodiac-zeden +Suggests: abyss, act, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, bamtools, beads, beast-mcmc, big-blast, bigsdb, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdna-db, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, concavity, conservation-code, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, edtsurf, eigensoft, elph, embassy-phylip, emboss-explorer, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fastqc, figaro, finex, fluctuate, forester, forge, galaxy, gassst, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, genometools, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, hmmer2, igv, jbrowse, jigsaw, jstreeview, kempbasu, lagan, lamarc, logol-bin, logomat-m, ltrsift, lucy, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, mosaik-aligner, mozilla-biofox, mpsqed, msatfinder, mugsy, mummergpu, murasaki, mview, ncbi-seg, ngila, norsnet, norsp, nw-align, oases, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, patristic, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phyloviz-core, phylowin, plato, prank, predictnls, predictprotein, proalign, profbval, profisis, profit, prot4est, pscan-tfbs, psipred, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatmasker, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, seqtk, sequenceconverter.app, sga, sift, smalt, snap, snpeff, soapdenovo, spice, splitstree, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tigr-glimmer-mg, tophat, trace2dbest, tracetuner, treebuilder3d, treetime, treeview, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zalign, zodiac-zeden Description: Debian Med micro-biology packages This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences. @@ -68,7 +68,7 @@ Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: bioperl, bioperl-run, biosquid, libace-perl, libai-fann-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbiococoa-dev, libbiojava-java, libbiojava3-java, libchado-perl, libffindex0-dev, libgenome-1.3-0-dev, libgo-perl, libhmsbeagle-dev, libjebl2-java, libncbi6-dev, libpal-java, librg-blast-parser-perl, librg-reprof-bundle-perl, librostlab-blast-doc, librostlab-blast0-dev, librostlab-doc, librostlab3-dev, libsort-key-top-perl, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, seqan-dev -Suggests: bioclipse, biostrings, iranges, libbamtools-dev, libbio-das-perl, libforester-java, libgbfp-dev, libgenometools0-dev, libgff-perl, libmems-1.5-1, libnhgri-blastall-perl, libopenmm4-dev, libqsearch-dev, librcsb-core-wrapper0-dev, libsbml5-dev, octace-bioinfo, octave-bioinfo, pysam, python-biom-format, python-librcsb-core-wrapper, python-mmtk, r-bioc-biocgenerics, r-cran-rocr +Suggests: bioclipse, biostrings, iranges, libbamtools-dev, libbio-das-perl, libforester-java, libgbfp-dev, libgenometools0-dev, libgff-perl, libmems-1.5-1, libnhgri-blastall-perl, libopenmm4-dev, libqsearch-dev, librcsb-core-wrapper0-dev, libsbml5-dev, libswarm2-dev, octace-bioinfo, octave-bioinfo, pysam, python-biom-format, python-librcsb-core-wrapper, python-mmtk, r-bioc-biocgenerics, r-cran-rocr Description: Debian Med packages for development of micro-biology applications This metapackage will install Debian packages which might be helpful for development of applications for micro-biological research. @@ -107,7 +107,7 @@ Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: epigrass, r-cran-diagnosismed, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epir, r-cran-epitools -Suggests: netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance, repast, swarm +Suggests: netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance, repast Description: Debian Med epidemiology related packages This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for @@ -157,7 +157,7 @@ This metapackage will install tools that are useful for radiation oncology. -Package: med-pharma +Package: med-pharmacy Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: chemtool diff -Nru debian-med-1.13ubuntu1/debian-med-tasks.desc debian-med-1.13.1ubuntu1/debian-med-tasks.desc --- debian-med-1.13ubuntu1/debian-med-tasks.desc 2012-11-19 20:38:20.000000000 +0530 +++ debian-med-1.13.1ubuntu1/debian-med-tasks.desc 2012-12-08 21:50:47.000000000 +0530 @@ -436,7 +436,7 @@ Packages: list dicompyler -Task: med-pharma +Task: med-pharmacy Section: debian-med Description: Debian Med packages for pharmaceutical research This metapackage contains dependencies for a @@ -444,7 +444,7 @@ pharmaceutical research. Relevance: 10 Key: - med-pharma + med-pharmacy Packages: list chemtool diff -Nru debian-med-1.13ubuntu1/tasks/bio debian-med-1.13.1ubuntu1/tasks/bio --- debian-med-1.13ubuntu1/tasks/bio 2012-11-19 20:38:20.000000000 +0530 +++ debian-med-1.13.1ubuntu1/tasks/bio 2012-12-08 21:50:47.000000000 +0530 @@ -225,6 +225,10 @@ Depends: paml Depends: ensembl +Pkg-URL: http://snapshot.debian.org/package/ensembl/63-1/ +Remark: Ensembl was removed from Debian due #645487 + Ensembl used to be in Debian experimental branch but was removed for formal reasons which + are explained in http://bugs.debian.org/645487 Depends: mrbayes @@ -435,6 +439,8 @@ Depends: pscan-tfbs +Depends: psipred + Depends: python-reaper Depends: r-other-valdar-bagphenotype.library diff -Nru debian-med-1.13ubuntu1/tasks/bio-dev debian-med-1.13.1ubuntu1/tasks/bio-dev --- debian-med-1.13ubuntu1/tasks/bio-dev 2012-11-19 20:38:20.000000000 +0530 +++ debian-med-1.13.1ubuntu1/tasks/bio-dev 2012-12-08 21:50:47.000000000 +0530 @@ -119,6 +119,8 @@ Depends: python-biom-format +Suggests: libswarm2-dev + Depends: bioclipse Homepage: http://www.bioclipse.net/ License: Eclipse Public License (EPL) + exception diff -Nru debian-med-1.13ubuntu1/tasks/bio-phylogeny debian-med-1.13.1ubuntu1/tasks/bio-phylogeny --- debian-med-1.13ubuntu1/tasks/bio-phylogeny 2012-11-19 20:38:20.000000000 +0530 +++ debian-med-1.13.1ubuntu1/tasks/bio-phylogeny 2012-12-08 21:50:47.000000000 +0530 @@ -99,27 +99,6 @@ Depends: treeview -Depends: phylographer -Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html -Responsible: Charles Plessy -WNPP: 426489 -License: GPL -X-Category: Graphical representation of sequence conservation -Language: Tcl/Tk -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phylographer/trunk/ -Pkg-Description: Graph Visualization Tool - PhyloGrapher is a program designed to visualize and study evolutionary - relationships within families of homologous genes or proteins - (elements). PhyloGrapher is a drawing tool that generates custom graphs - for a given set of elements. In general, it is possible to use - PhyloGrapher to visualize any type of relations between elements. - Used in conjunction with tcl_blast_parser, PhyloGrapher can represent - the results of a BLAST search as a graph. - . - PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST - biological sequence alignment reports (BLAST is provided by Debian's - blast2 package). - Depends: phylowin Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html WNPP: 395840 diff -Nru debian-med-1.13ubuntu1/tasks/epi debian-med-1.13.1ubuntu1/tasks/epi --- debian-med-1.13ubuntu1/tasks/epi 2012-11-19 20:38:20.000000000 +0530 +++ debian-med-1.13.1ubuntu1/tasks/epi 2012-12-08 21:50:47.000000000 +0530 @@ -71,12 +71,12 @@ http://www.tbiomed.com/content/5/1/11 http://lists.debian.org/debian-med/2009/08/msg00013.html (and following mails) -Suggests: swarm -Homepage: http://www.swarm.org/ -License: GPL -WNPP: 179182 -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/swarm/trunk/ -Pkg-Description: multi-agent simulation of complex systems +X-Suggests: swarm +X-Homepage: http://www.swarm.org/ +X-License: GPL +X-WNPP: 179182 +X-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/swarm/trunk/ +X-Pkg-Description: multi-agent simulation of complex systems Swarm is a software package for multi-agent simulation of complex systems, originally developed at the Santa Fe Institute. Swarm is intended to be a useful tool for researchers in a variety of diff -Nru debian-med-1.13ubuntu1/tasks/imaging-dev debian-med-1.13.1ubuntu1/tasks/imaging-dev --- debian-med-1.13ubuntu1/tasks/imaging-dev 2012-11-19 20:38:20.000000000 +0530 +++ debian-med-1.13.1ubuntu1/tasks/imaging-dev 2012-12-08 21:50:47.000000000 +0530 @@ -58,6 +58,8 @@ Depends: python-nitime +Depends: python-casmoothing + Depends: libvia-dev Depends: odin @@ -150,29 +152,7 @@ ; Added by blends-inject 0.0.7. [Removed unneeded publication dat] Depends: libbiosig-dev -Depends: libctkcore0-dev -Homepage: http://commontk.org -License: Apache 2.0 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/commontk/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/commontk/trunk/ -WNPP: 617337 -Pkg-Description: Common ToolKit for medical image analysis - The Common Toolkit is a community effort to provide support code for medical - image analysis, surgical navigation, and related projects. - The goal of CTK are as follows: - Provide a unified set of basic programming constructs that are useful for - medical imaging applications development - . - Facilitate the exchange and combination of code and data - . - Document, integrate, and adapt successful solutions - . - Avoid the duplication of code and data - . - Continuously extend to new tasks within the scope of the toolkit (medical - imaging) without burdening existing tasks - . - This is the CTK Core plugin development files +Depends: libctk-dev ; Added by blends-inject 0.0.7. [now official package] Depends: python-cfflib diff -Nru debian-med-1.13ubuntu1/tasks/pharma debian-med-1.13.1ubuntu1/tasks/pharma --- debian-med-1.13ubuntu1/tasks/pharma 2012-07-20 16:33:56.000000000 +0530 +++ debian-med-1.13.1ubuntu1/tasks/pharma 1970-01-01 05:30:00.000000000 +0530 @@ -1,16 +0,0 @@ -Task: Pharmacology -Description: Debian Med packages for pharmaceutical research - This metapackage contains dependencies for a - collection of software and documentation which is useful for - pharmaceutical research. - -Depends: chemtool - -Depends: raccoon - -Comment: Several related R packages are listed at CRAN: - http://cran.r-project.org/web/views/Pharmacokinetics.html - Specifically these might be of interest: - http://cran.r-project.org/web/packages/PK/index.html - http://cran.r-project.org/web/packages/PKfit/index.html - http://cran.r-project.org/web/packages/PKtools/index.html diff -Nru debian-med-1.13ubuntu1/tasks/pharmacy debian-med-1.13.1ubuntu1/tasks/pharmacy --- debian-med-1.13ubuntu1/tasks/pharmacy 1970-01-01 05:30:00.000000000 +0530 +++ debian-med-1.13.1ubuntu1/tasks/pharmacy 2012-11-27 22:09:43.000000000 +0530 @@ -0,0 +1,16 @@ +Task: Pharmacology +Description: Debian Med packages for pharmaceutical research + This metapackage contains dependencies for a + collection of software and documentation which is useful for + pharmaceutical research. + +Depends: chemtool + +Depends: raccoon + +Comment: Several related R packages are listed at CRAN: + http://cran.r-project.org/web/views/Pharmacokinetics.html + Specifically these might be of interest: + http://cran.r-project.org/web/packages/PK/index.html + http://cran.r-project.org/web/packages/PKfit/index.html + http://cran.r-project.org/web/packages/PKtools/index.html diff -Nru debian-med-1.13ubuntu1/tasks/practice debian-med-1.13.1ubuntu1/tasks/practice --- debian-med-1.13ubuntu1/tasks/practice 2012-11-19 20:38:20.000000000 +0530 +++ debian-med-1.13.1ubuntu1/tasks/practice 2012-12-08 21:50:47.000000000 +0530 @@ -23,11 +23,11 @@ Depends: entangle Depends: freeicd -Homepage: http://www.freemedforms.com/ -License: GPL3 -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/freeicd/trunk/ -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/freeicd/trunk/ -Pkg-Description: ICD10 coding assistant +X-Homepage: http://www.freemedforms.com/ +X-License: GPL3 +X-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/freeicd/trunk/ +X-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/freeicd/trunk/ +X-Pkg-Description: ICD10 coding assistant FreeICD is the result of FreeMedForms ICD10 assistant plugins built into a standalone application. It is developed by medical doctors and is intended for use by these same professionals. It can be used @@ -281,16 +281,7 @@ http://thera-pi.cvs.sourceforge.net/viewvc/thera-pi/ . Depends: freeshim -Homepage: http://freeshim.org/ -License: GPL -Language: Java Pkg-URL: https://launchpad.net/~rufustfirefly/+archive/ppa/+buildjob/2489799/+files/shim_0.1.1-1ubuntu2~maverick_all.deb -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/shim/trunk -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/shim/trunk/ -Pkg-Description: medical device interface layer - FreeSHIM allows multiple medically-related peripheral devices to be exposed - to an EMR/PM system simply by installing FreeSHIM on each workstation - with connected devices and configuring a single configuration file! Remark: Needs Java prerequisites Missing Java prerequisites in Debian: * org.hsqldb:hsqldb:2.0.0